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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jun 23, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.

Shuoyong Shi1, Bhadrachalam Chitturi, Nick V Grishin

  • 1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA.

Nucleic Acids Research
|May 8, 2009
PubMed
Summary
This summary is machine-generated.

ProSMoS is a new web server for protein structure pattern searching. It identifies three-dimensional (3D) motifs based on secondary structural element (SSE) architecture and topology, aiding in functional and evolutionary studies.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein structure comparison is crucial for understanding protein function and evolution.
  • Existing methods often focus on coordinate superposition or contact similarity, not motif-based analysis.
  • A gap exists in web servers for identifying 3D structural motifs based on secondary structural element (SSE) topology.

Purpose of the Study:

  • To develop and implement a web server for protein structure pattern searching.
  • To enable the identification of 3D structural motifs independent of precise coordinates.
  • To provide a tool for analyzing general and distant structural similarities in proteins.

Main Methods:

  • Developed the ProSMoS (Protein Structure Motif Search) approach and web server.
  • Represented 3D protein structures as interaction matrices.
  • Included SSE types, connectivity, handedness, and beta-sheet definitions in the representation.

Main Results:

  • ProSMoS successfully converts 3D structures into a comprehensive interaction matrix.
  • The server can search a database for user-defined structural patterns.
  • Identified structural patterns based on SSE architecture and topology.

Conclusions:

  • ProSMoS addresses the need for motif-based protein structure searches.
  • The server facilitates the discovery of general and distant structural similarities.
  • ProSMoS is a valuable tool for structural biologists in functional and evolutionary research.